Palmer Penguins

This example uses the Palmer Penguins data set: https://github.com/allisonhorst/palmerpenguins.

Look At The Data

library(palmerpenguins) # penguin data

library(pander) # nicely formatted tables

pander(head(penguins)) # nicely formatted table of top of data

Table continues below
species	island	bill_length_mm	bill_depth_mm	flipper_length_mm
Adelie	Torgersen	39.1	18.7	181
Adelie	Torgersen	39.5	17.4	186
Adelie	Torgersen	40.3	18	195
Adelie	Torgersen	NA	NA	NA
Adelie	Torgersen	36.7	19.3	193
Adelie	Torgersen	39.3	20.6	190

body_mass_g	sex	year
3750	male	2007
3800	female	2007
3250	female	2007
NA	NA	2007
3450	female	2007
3650	male	2007

Calculate a Correlation

We calculate the correlation of body mass and flipper length.

We need to use the option use = "complete.obs" to avoid an error message because some observations have missing data.

cor(penguins$body_mass_g, 
    penguins$flipper_length_mm,
    use = "complete.obs")

[1] 0.8712018

There is some indication that penguins with higher body mass have longer flippers.

To get a more nicely formatted correlation value, we can read this correlation into a variable, and then print out this correlation as part of a sentence in inline code. See this RMarkdown document for how this is done, or take a look at this page from RStudio.

mycorrelation <- cor(penguins$body_mass_g, 
                     penguins$flipper_length_mm,
                     use = "complete.obs")

The value of the correlation is 0.8712018.

Graphing

Base R

Basic Base R Plot

plot(penguins$body_mass_g, 
    penguins$flipper_length_mm)

Advanced Base R Plot

plot(penguins$body_mass_g, 
    penguins$flipper_length_mm,
    col = "blue",
    pch = 19, # Plotting CHaracter
    xlab = "body mass",
    ylab = "flipper length",
    main = "Penguin Body Mass and Flipper Length")

ggplot

library(ggplot2)

ggplot(penguins,
       aes(x = body_mass_g,
           y = flipper_length_mm)) +
  geom_point() +
  geom_smooth() +
  labs(title = "Penguin Body Mass and Flipper Length",
       x = "body mass",
       y = "flipper length")

Citation

Gorman KB, Williams TD, Fraser WR (2014). Ecological Sexual Dimorphism and Environmental Variability within a Community of Antarctic Penguins (Genus Pygoscelis). PLoS ONE 9(3): e90081. https://doi.org/10.1371/journal.pone.009008

Calculating and Graphing Correlations in R